Inputs for the phasing module

[philil...@gmail.com]

Hi

I'm interested in using the phasing module, but I'm not sure where the input files come from.

I see run-hic-phaser.sh takes a vcf and mnd file. My understanding is that you:

- Contig WGS reads -> fasta

- Run juicer using contig fasta and HiC reads -> mnd file

- Run a variant caller using HiC reads aligned to contig fasta, and contig fasta as reference -> vcf file

From the Hoencamp et al. 2021 Science paper, I see you used DRAGEN to call variants, but I assume any variant caller will do (eg DeepVariant, GATK, etc)?

Does run-hic-phaser.sh create a fasta file that can be be used to integrate back into the standard run-asm-pipeline.sh? I can only see it creating a vcf and assembly file.

Sorry for all the simple questions.

Best wishes

Philip

[Olga Dudchenko]

Hi Philip,

You only need to contig reads if you don't have a reference assembly: if you are running for something like human you can use hg38 etc.

Yes, any SNP caller would do. We've worked with GATK and Dragen.

No, the phaser does not create a fasta file. It will dump an updated vcf file, with phasing information, and some phasing contact maps.

Best,

Olga